Algorithms for Bioinformatics

Type of study	Doctoral
Language of instruction	English
Code	460-6025/02
Abbreviation	ABI
Course title	Algorithms for Bioinformatics
Credits	10
Coordinating department	Department of Computer Science
Course coordinator	prof. RNDr. Václav Snášel, CSc.

Subject syllabus

• Sequence similarity
• Suffix trees
• Genome alignment and multiple sequence alignment
• Database search
• Phylogeny Reconstruction and Comparison
• Genome Rearrangement
• Motif Finding
• RNA secondary structure prediction
• Peptide Sequencing
• Population genetics
• BAM algorithm for resequencing, BLAST and BLAT algorithms description
• Assembly algoritms, paired-end scaffolding algorithms

Literature

• Sung, W. K. (2009). Algorithms in bioinformatics: A practical introduction. CRC Press.
• Compeau, Phillip, and Pavel Pevzner. Bioinformatics algorithms: an active learning approach. Vol. 1. La Jolla: Active Learning Publishers, 2015.
• Zvelebil, Marketa J., and Jeremy O. Baum. Understanding bioinformatics. Garland Science, 2007.

Advised literature

• M. Dorigo, T. Stützle, Ant Colony Optimization, MIT Press, Cambridge, MA, 2004.
• A. Engelbrecht, Computational Intelligence: An Introduction, 2nd Edition, Wiley, New York, NY, USA, 2007.

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